MolNFT v1 · #131300 · protein
Ligand binding to farnesoid-X-receptor
5Q13 · Bile acid receptor: “Ligand binding to farnesoid-X-receptor”. X-ray diffraction, 1 ligand (9MD), 5 pockets (best druggability 0.85). MolNFT v1 #131300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Q13
- Type
- protein
- Length
- 483 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bile acid receptor; Coactivator peptide src-1 HD3
- UniProt
- Q96RI1, A8K1V4
- Ligands
- 9MD
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bile acid receptor | protein | 232 | 72% helix, 0% strand | Q96RI1 |
| B | Coactivator peptide src-1 HD3 | protein | 10 | 70% helix, 0% strand | A8K1V4 |
| C | Bile acid receptor | protein | 230 | 72% helix, 0% strand | Q96RI1 |
| D | Coactivator peptide src-1 HD3 | protein | 11 | 73% helix, 0% strand | A8K1V4 |
Ligands and binding sites
- 9MD · (2S)-2-[6-chloro-2-(4-chlorophenyl)-5-fluoro-1H-benzimidazol-1-yl]-N-cyclohexyl-2-[(2S)-oxan-2-yl]acetamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.85 | 0.94 | 38 | 9MD |
| 2 | 440 | 0.84 | 0.91 | 45 | 9MD |
| 3 | 141 | 0.48 | 0.78 | 20 | empty |
| 4 | 144 | 0.43 | 0.75 | 23 | empty |
| 5 | 73 | 0.33 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–D · 620 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 554 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 464 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5Q13 · Ligand binding to FARNESOID-X-RECEPTOR · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q96RI1
- Every structure of UniProt A8K1V4
- Elsewhere: RCSB PDB 5Q13 · PDBe 5Q13 · UniProt Q96RI1 · UniProt A8K1V4
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